2d3t: Difference between revisions

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-[[Image:2d3t.gif|left|200px]]
- {{Structure
+==Fatty Acid beta-oxidation multienzyme complex from Pseudomonas Fragi, Form V==
-|PDB= 2d3t |SIZE=350|CAPTION= <scene name='initialview01'>2d3t</scene>, resolution 3.4&Aring;
+<StructureSection load='2d3t' size='340' side='right'caption='[[2d3t]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene> and <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
+<table><tr><td colspan='2'>[[2d3t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3T FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Acetyl-CoA_C-acyltransferase Acetyl-CoA C-acyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.16 2.3.1.16]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-}}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3t OCA], [https://pdbe.org/2d3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3t RCSB], [https://www.ebi.ac.uk/pdbsum/2d3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FADB_PSEFR FADB_PSEFR] Involved in the aerobic and anaerobic degradation of long-chain fatty acids via beta-oxidation cycle. Catalyzes the formation of 3-oxoacyl-CoA from enoyl-CoA via L-3-hydroxyacyl-CoA. It can also use D-3-hydroxyacyl-CoA and cis-3-enoyl-CoA as substrate.[HAMAP-Rule:MF_01621]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3t_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d3t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an intermediate structure of the complex among the previously reported structures. However, the theoretical scattering curves calculated from the crystal structures remarkably disagree with the experimental profiles. Instead, an ensemble of the atomic models, which were all calculated by rigid-body optimization, reasonably explained the experimental data. These structures significantly differ from those in the crystals, but they maintain the substrate binding pocket at the domain boundary. Comparisons among these structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide adenine dinucleotide induces domain rearrangements in the complex. The conformational changes suggest the structural events occurring during the chain reaction catalyzed by the multienzyme complex.
-'''Fatty Acid beta-oxidation multienzyme complex from Pseudomonas Fragi, Form V'''
+Ligand-induced domain rearrangement of fatty acid beta-oxidation multienzyme complex.,Tsuchiya D, Shimizu N, Ishikawa M, Suzuki Y, Morikawa K Structure. 2006 Feb;14(2):237-46. PMID:16472743<ref>PMID:16472743</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2d3t" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The quaternary structure of a fatty acid beta-oxidation multienzyme complex, catalyzing three sequential reactions, was investigated by X-ray crystallographic and small-angle X-ray solution scattering analyses. X-ray crystallography revealed an intermediate structure of the complex among the previously reported structures. However, the theoretical scattering curves calculated from the crystal structures remarkably disagree with the experimental profiles. Instead, an ensemble of the atomic models, which were all calculated by rigid-body optimization, reasonably explained the experimental data. These structures significantly differ from those in the crystals, but they maintain the substrate binding pocket at the domain boundary. Comparisons among these structures indicated that binding of 3-hydroxyhexadecanoyl-CoA or nicotinamide adenine dinucleotide induces domain rearrangements in the complex. The conformational changes suggest the structural events occurring during the chain reaction catalyzed by the multienzyme complex.
+*[[Thiolase 3D structures|Thiolase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-D3T is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3T OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Ligand-induced domain rearrangement of fatty acid beta-oxidation multienzyme complex., Tsuchiya D, Shimizu N, Ishikawa M, Suzuki Y, Morikawa K, Structure. 2006 Feb;14(2):237-46. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16472743 16472743]
-[[Category: Acetyl-CoA C-acyltransferase]]
-[[Category: Protein complex]]
 [[Category: Pseudomonas fragi]]
-[[Category: Ishikawa, M.]]
+[[Category: Ishikawa M]]
-[[Category: Morikawa, K.]]
+[[Category: Morikawa K]]
-[[Category: Shimizu, N.]]
+[[Category: Shimizu N]]
-[[Category: Suzuki, Y.]]
+[[Category: Suzuki Y]]
-[[Category: Tsuchiya, D.]]
+[[Category: Tsuchiya D]]
-[[Category: ACO]]
-[[Category: NAD]]
-[[Category: alpha2beta2 heterotetrameric complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:23:00 2008''